Shadows
by lynnemari
Summary: Set in Season 3. Life as Booth and Brennan know it is gone. Together they must survive and figure out the mystery that lingers in the shadows. Note: This is a first time fanfic so I'm sorry if the writing isn't the best, bear with :')
1. Chapter 1

Sirens blazing, alarms ringing, smoke choking. Everywhere she turned Brennan was trapped. Stumbling she gathered her strength and tried to stand up, it was hard. Her head spun from what she assumed was some kind of collision injury but she couldn't be certain. Booth, where was Booth? She had to find him.

Scanning the chaos she saw others like her, calling out for loved ones. But she couldn't be sure, was she even screaming? Looking up she saw the remnants of the FBI Headquarters, tattered and torn, angry like a papier-mâché project it barely stood. Her lips were dry and licking them she found the hot, sticky, metallic taste of blood. Dazed, disorientated, determined she tried calling out for him again. Her voice was raw and scratchy, but at least it made a sound. Too many minuets had passed since the explosion. Yet suddenly out of the haze of sirens came her partner. "Bones, where the hell have you been? Are you ok that looks like a pretty bad head wound you got there?" Yes she was injured, she remembered.

"I'm ok Booth, just a few abrasions and a minor concussion." But he wasn't convinced, urgency was in his eyes. "Bones you're hardly making sense here but we have to get out they're quarantining people and last I heard the state was in control of the army." State, army the concepts seemed fuzzier and fuzzier as her mind slowly drifted away.

Booth watched his partner quickly loose balance and her consciousness in front of him. Without thinking he picked her up. More sirens were coming and well, he didn't know what the hec that meant but he knew that he needed to get his partner out of there before the situation escalated. Quickly he turned and ran towards the workman's back exit, that he knew should be clear. Holding Brennan tightly he heard gunfire retreating in the distance, police called code 323. That could mean only one thing. Bio-terrorism.

Bones shifted in his arms, still mumbling and grumbling which reassured him. His car was out back and they could take the country roads to his friends hunting cabin. For now they'd be alright.

* * *

><p>The gentle humming of the SUV woke Brennan first and for a moment she felt secure, and safe. But this brief naivety was quickly lost. Her mind flashed back to images of the explosion and fires. What was going on? "Booth.." "Booth where are we?"<br>"Bones oh my god! Thank goodness you woke up, I was getting real worried about you."  
>"You didn't answer my question Booth?"<br>"Oh yeah, about that. We're kind of on the run at the moment. After the Hoover exploded the cops were calling 323, that stands for a bio-terrorist emergency."  
>"I know what it stands for Booth" she gave him a small grin.<br>"Should've figured, what with your crazy security clearances and all. But the point is they were quarantining the area and last I overheard the MOD had taken over, which is never good." His eyes were downcast, face pale with worry.  
>"But what I thought you liked the army, why did we leave?" This wasn't making sense to her, the Booth she knew had almost blind faith in the government and justice system. "You're right, I did but the situation changed. You're not gonna like what I'm about to tell you Bones."<p>

"What is it Booth, c'mon you can tell me." He pulled over the car.  
>"Bones, for the past 18 months I've been involved in a very hush hush operation."<br>"Hush hush, I don't know what that means?" Her brows furrowed, Brennan was completely lost.  
>"It means it was highly classified, only a handful of agents, myself and a biomedical lab team were involved." Booth could tell she wanted to interject but he continued on. "It had to be that way Bones." he reassured her. "We were investigating rumours of serious virus that can alter neurological pathways at rates never before seen. It literally changes peoples personality. The main catch here is that current intel tells us its corrupt Feds who have been illegally experimenting with it"<p>

Brennan observed him thoughtfully for a moment. " I understand, I too work for a separate government agency. You could not have told me." Booth noted despite her accepting statement, pain hid behind her words. "I assume the virus you mention is the one associated with the biological quarantining of the Hoover. If so how come we're not effected, do you think the virus was released?"  
>" Most likely yes. You however are safe. I vaccinated you."<br>"What! When?" Brennan was not at all comfortable with this new knowledge.  
>"Ok well we're not sure if it's 100% effective, it was barely at clinical trials. But umm I may have given it to you in your sleep."<br>"What, how would you have even accomplished that, I'm a very light sleeper and you haven't slept at my apartment at all since? Oh no you didn't" Booth squirmed in his seat. "Your "Special" hot cocoa! You drugged me, then injected me with the vaccine. Unbelievable."  
>"I really couldn't let you know about this Bones, I trust you with my life but this way was safer. For everyone." Booth sighed.<p>

"But what about everyone else?"  
>"Parker and Rebecca were vaccinated, they didn't question much when I mentioned something to do with working amongst remains"<br>"Wow" This situation sounded more dire than she originally thought; the explosions at the Hoover, that was just the beginning. The virus and the chaos it was bringing probably would not be localised for long. "This virus, how quickly does it spread." She questioned.  
>"Here, I'll give you the pathology file. It's a class A H1PV virus, similar to the flu or the common cold except it's target binding sites are on the nerve cells"<br>She glanced at him, seeing Booth in such a scientific context unsettled her.  
>"Ok I'll read through it now. Where are we heading?"<br>"My friends cabin, he never goes there I stocked it full with supplies too." Booth started the car. "We have about a four hour drive ahead of us, sorry we can't use the main roads so it might be a bit bumpy."

He looked over at Brennan. She was already well engrossed in the file, happy it would keep her stated. Booth knew however that this part of his life he had been keeping from her wasn't a solved issue by any means.


	2. Chapter 2

The SUV was warming up finally after their stop on the road. Brennan was silent, she gazed out the condensated glass imaging the chaos that would soon envelope the rest of north america, assuming her approximations were correct. She wondered if Angela and Hodgins were alright, and Zack, dear Zack. Only time would tell and she wasn't sure if she was going to like what it told.

"Bones, we're here now." Brennan looked up at him with a doe like expression.  
>"Ok" was all she replied. Booth led her out of the car, his hand tentatively touching the small of her back.<br>"Well I know it's not much but this is it, where we're probably gonna have to live until this is over." Bones just looked at him, the gravity of their situation was really sinking in now, yet the medium sized log cabin did look somewhat inviting at this point. It was shelter.

When she stepped through the door, Brennan was shocked. The interior of the cabin was beautiful, all polished wood with some native american rugs and throws. The Living room had a cosy sofa and fire place with a hand carved wooden table. Behind it lay the kitchen which she soon found out was a lot more modern than it seemed. "Wow Booth. This is Lovely." He didn't say anything but took her hand and led her to a door that looked like the opening to a coat closet. He opened it and thus revealed a stair case? OK even Brennan knew that most cabins didn't have a basement. But apparently this one did.

They turned the corner and Booth flicked on the lights.

Brennan couldn't believe it, she was essentially in a downscale version of the lab. It had everything from the mass spec to a few pieces of equipment she had only read about. "Where could you have possibly obtained such equipment Booth?"

"Well, I told you there weren't many people involved in the investigation but the ones that were, well let's just say they had connections." Brennan had to admit, she was impressed. Despite the lingering hurt from his secrecy Booth really did run a tight operation.

"I assume you'll be using this place to figure the treatment for the disease?"  
>"Yep, that's what it was built for."<br>"But I don't understand, my knowledge of immunology is oxidised iron at best."  
>"Umm well, I figure since you did get your second PhD in it you'd be good enough, plus you're a genius Bones" She fought a rising blush at his compliment, though the pressure was unnerving. She knew they'd found the basic antibody of the virus according to the report but that was minuscule in the amount of work that would have to progress.<p>

"Booth I'm not sure about this." She looked up at him, and Booth detected a hint of genuine worry behind her eyes.  
>"I know Bones but trust me, the findings so far are solid and if we're lucky we might be able to contact the previous team that was working on this.<br>"But I'm not a team Booth, I'm just one person. A forensic anthropologist. I don't know if I can do this." Her lip quivered, Booth knew she'd just been through hell and back finding out all of this after practically being blown up.

"Bones look at me." She tilted her chin, there eyes were locked now in a deep transfixion. "We can do this, OK. I promise. You're the best scientist I know, probably the best person I've met. We're gonna get through this" She couldn't say much, instead booth pulled her into a fierce embrace. He held her and she him for what seemed like an eternity.

"I'm tired Booth."  
>"All right, let's get to bed." He held her hand, guiding her back up the stairs and into the master bedroom. " I can umm, sleep on the sofa if you want?"<br>"I don't mind, it wouldn't be the first time" Both their minds flickered back to the few undercover cases, sharing motel and hotel rooms.  
>"Yeah you're right." Plus Booth want entirely opposed to sharing a bed with his beautiful partner.<p>

"Night Bones."  
>"Good night Booth."<p>

And just like that both of them slipped into a deep and dreamless sleep.


End file.
